Do you have to fill in all the bubbles on a ballot for your vote to count? Say I'm undecided on 1 candidate or one of the two questions? Can I skip it?

Leaving certain lines on the ballot empty will not affect those candidates you do vote for, this called an 'undervote'. Only voting for opposing candidates will negate your vote for that particular office.

Presidential elections is when the undervote is the largest, voters go in determined to vote for president and leave the rest of the ballot blank. This is due in large part to the news coverage of the presidential race, even though state races have far greater effect on citizens lives, they don't garner the attention that the presidential race gets.